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- PDB-3bu6: Crystal structure of the insulin receptor kinase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3bu6
TitleCrystal structure of the insulin receptor kinase in complex with IRS2 KRLB phosphopeptide
Components
  • Insulin receptor substrate 2
  • insulin receptor subunit beta
KeywordsTRANSFERASE / IR / IRK / IRS-2 / KRLB / insulin receptor / phosphopeptide / Alternative splicing / ATP-binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / Tyrosine-protein kinase / Transducer
Function / homology
Function and homology information


IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / SOS-mediated signalling / PI3K/AKT activation / positive regulation of type B pancreatic cell proliferation / Erythropoietin activates RAS / PI3K Cascade / Interleukin-7 signaling / IRS activation ...IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / SOS-mediated signalling / PI3K/AKT activation / positive regulation of type B pancreatic cell proliferation / Erythropoietin activates RAS / PI3K Cascade / Interleukin-7 signaling / IRS activation / Signal attenuation / negative regulation of kinase activity / epithelial cell migration / negative regulation of long-chain fatty acid import across plasma membrane / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / RAF/MAP kinase cascade / PIP3 activates AKT signaling / cellular response to peptide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of female gonad development / positive regulation of meiotic cell cycle / RET signaling / phosphatidylinositol 3-kinase activator activity / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / positive regulation of developmental growth / type B pancreatic cell proliferation / male sex determination / insulin receptor complex / insulin-like growth factor I binding / mammary gland development / transmembrane receptor protein tyrosine kinase adaptor activity / exocrine pancreas development / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cargo receptor activity / positive regulation of mesenchymal cell proliferation / insulin binding / negative regulation of B cell apoptotic process / neuronal cell body membrane / adrenal gland development / PTB domain binding / Signaling by Insulin receptor / IRS activation / positive regulation of respiratory burst / amyloid-beta clearance / regulation of embryonic development / positive regulation of receptor internalization / protein kinase activator activity / insulin receptor substrate binding / positive regulation of epithelial cell migration / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / transport across blood-brain barrier / response to glucose / heart morphogenesis / activation of protein kinase B activity / Insulin receptor recycling / insulin-like growth factor receptor binding / 14-3-3 protein binding / positive regulation of B cell proliferation / dendrite membrane / neuron projection maintenance / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / insulin-like growth factor receptor signaling pathway / positive regulation of glycolytic process / learning / positive regulation of D-glucose import / insulin receptor binding / placental growth factor receptor activity / cellular response to glucose stimulus / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / brain development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of insulin secretion / caveola / receptor internalization / memory / cellular response to insulin stimulus / male gonad development
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / PH domain / PH domain profile. / Pleckstrin homology domain. / Growth factor receptor cysteine-rich domain superfamily / Pleckstrin homology domain / Fibronectin type III domain / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Insulin receptor / Insulin receptor substrate 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWu, J. / Hubbard, S.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2.
Authors: Wu, J. / Tseng, Y.D. / Xu, C.F. / Neubert, T.A. / White, M.F. / Hubbard, S.R.
History
DepositionDec 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: insulin receptor subunit beta
B: Insulin receptor substrate 2


Theoretical massNumber of molelcules
Total (without water)36,8292
Polymers36,8292
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.738, 84.724, 51.349
Angle α, β, γ (deg.)90.00, 113.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein insulin receptor subunit beta / IR / CD220 antigen


Mass: 35033.660 Da / Num. of mol.: 1 / Fragment: protein kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein/peptide Insulin receptor substrate 2 / IRS-2 / 4PS


Mass: 1795.748 Da / Num. of mol.: 1 / Fragment: UNP residues 620-634 / Source method: obtained synthetically
Details: The sequence of this peptide natually exists in Mus Musculus.
References: UniProt: P81122
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG8000 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorDetector: CCD / Date: Sep 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 26660 / Num. obs: 25301 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 12
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.1 / Num. unique all: 26660 / Rsym value: 0.332 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.908 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23858 1339 5 %RANDOM
Rwork0.20021 ---
obs0.20213 25301 98.47 %-
all-26660 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20.36 Å2
2---0.84 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 0 213 2690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222534
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9713437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30223.967121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67515427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3221518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021936
X-RAY DIFFRACTIONr_nbd_refined0.1840.21205
X-RAY DIFFRACTIONr_nbtor_refined0.30.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.212
X-RAY DIFFRACTIONr_mcbond_it0.6151.51599
X-RAY DIFFRACTIONr_mcangle_it0.99522491
X-RAY DIFFRACTIONr_scbond_it1.63531074
X-RAY DIFFRACTIONr_scangle_it2.5014.5946
LS refinement shellResolution: 1.95→1.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 107 -
Rwork0.266 1835 -
obs--98.08 %

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